permutation.moments.a {CNull}R Documentation

Given a matrix and an alpha diversity measure f, calculates the mean and variance of f based on the permutation (SIM2) null model

Description

Given a matrix M and an alpha diversity measure f, the function computes the mean and variance of f for a row in M, when M is shuffled according to the permutation model. The returned mean and variance is the same for every row in M. This is because the examined null model produces the same distribution for all rows in M; after shuffling M, each row has the same probability to store a specific community as any other row in the resulting matrix.

Usage

permutation.moments.a(matrix,f,args,reps=1000)

Arguments

matrix

A matrix with integer values. The matrix should not contain any NA values.

f

An alpha diversity function f. The interface of f should be such that f(matrix,args) returns a numeric vector V where the i-th element of V is equal to the value of f when applied at the i-th row of the given matrix. To fit to this interface, the user might have to develop f as a wrapper around an existing R function (see Examples).

args

A list with extra arguments needed by f.

reps

The number of randomizations. This argument is optional and its default value is set to one thousand.

Value

A list with two real numbers; the mean and the variance of f on the given matrix for the permutation model.

Author(s)

Constantinos Tsirogiannis (tsirogiannis.c@gmail.com)

References

Gotelli, N. J., 2000. Null Model Analysis of Species Co-Occurrence Patterns. Ecology, 81(9), pp.2606-2621.

Tsirogiannis, C., A. Kalvisa, B. Sandel and T. Conradi. Column-Shuffling Null Models Are Simpler Than You Thought. To appear.

See Also

permutation.pvalues.a

Examples

#In the next example null-model calculations are
#performed using a function of phylogenetic diversity.
#Hence, we first load the required packages.
require(CNull)
require(ape)
require(PhyloMeasures)

#Load phylogenetic tree of bird families from package "ape"
data(bird.families, package = "ape")

#Create 100 random communities with 50 families each
comm = matrix(0,nrow = 100,ncol = length(bird.families$tip.label))
for(i in 1:nrow(comm)) {comm[i,sample(1:ncol(comm),50)] = 1}
colnames(comm) = bird.families$tip.label

#Set function f to be the Phylogenetic Diversity measure (PD)
#as defined in the R package PhyloMeasures.
my.f = function(mt,args){ return (pd.query(args[[1]],mt))}

# This function takes one extra argument, which is a phylogenetic tree.
# Hence, create a list whose only element is the desired tree.
arguments = list()
arguments[[1]] = bird.families

# Calculate the mean and variance of f in the permutation null
# model using 2000 Monte Carlo randomizations
permutation.moments.a(comm,f=my.f,args=arguments,reps=2000)

[Package CNull version 1.0 Index]